LAMMPS (22 Oct 2020)
  using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture

units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
  1 molecules
  6 atoms with max type 1
  6 bonds with max type 1
  6 angles with max type 1
  6 dihedrals with max type 1
  0 impropers with max type 0
atom_style molecular

pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic

lattice sc 6.0
Lattice spacing in x,y,z = 6.0000000 6.0000000 6.0000000
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6                  extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
Created orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
  1 by 1 by 1 MPI processor grid

create_atoms 0 box mol cychex 734594
Created 3072 atoms
  create_atoms CPU = 0.003 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
  create_atoms CPU = 0.000 seconds

mass 1 14.027
mass 2 16.043

pair_coeff 1 1  0.1180  3.905
pair_coeff 2 2  0.2940  3.730

bond_coeff      1  260.00 1.5260
angle_coeff     1  63.0   112.40
dihedral_coeff  1  2.0 1 3

thermo 100
minimize 0.001 0.001 500 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 7 7 7
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.28 | 12.28 | 12.28 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            0 4.3897851e+13    341.92144 4.3897851e+13 1.0886888e+14 
     100            0   -4351.8383    516.49891   -3835.3394    11635.037 
     190            0   -6191.8175    457.61209   -5734.2054     4365.373 
Loop time of 3.46057 on 1 procs for 190 steps with 3872 atoms

99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final = 
      43897850768892.8  -5729.17187196146  -5734.20542785978
  Force two-norm initial, final = 1.1080994e+15 72.746805
  Force max component initial, final = 4.6607099e+14 17.394645
  Final line search alpha, max atom move = 0.0041634525 0.072421779
  Iterations, force evaluations = 190 297

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 3.0573     | 3.0573     | 3.0573     |   0.0 | 88.35
Bond    | 0.10271    | 0.10271    | 0.10271    |   0.0 |  2.97
Neigh   | 0.26654    | 0.26654    | 0.26654    |   0.0 |  7.70
Comm    | 0.013532   | 0.013532   | 0.013532   |   0.0 |  0.39
Output  | 3.3796e-05 | 3.3796e-05 | 3.3796e-05 |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.02041    |            |       |  0.59

Nlocal:        3872.00 ave        3872 max        3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        12122.0 ave       12122 max       12122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:       774375.0 ave      774375 max      774375 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 774375
Ave neighs/atom = 199.99354
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0

velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Per MPI rank memory allocation (min/avg/max) = 11.16 | 11.16 | 11.16 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0          100   -6191.8175    457.61209   -4580.3339    4842.3161 
     100    106.81295   -5670.2783    921.20332   -3516.5907    5959.5039 
     200    119.22024   -5701.0103    1040.0336   -3285.3283    6755.0994 
     300    127.23574   -5706.7587    1023.9882   -3214.6335    6081.4162 
     400     133.7471   -5734.1781    1113.1696   -3077.7387    6569.8751 
     500    138.72092   -5756.3282    1191.5668   -2964.1003    6433.1441 
     600    149.02612   -5731.7291    1205.3124   -2806.8466     6366.853 
     700     153.5469   -5670.5879    925.61956   -2973.2344    7677.5226 
     800    163.38118   -5629.0757    1180.6507    -2563.216    5865.8079 
     900    173.27279   -5639.6903    1160.2138    -2480.131    8168.7364 
    1000    178.05354   -5579.0492    913.19337   -2611.3466    6220.8001 
    1100    188.99752   -5551.4873    1178.9541   -2191.7446    7734.6527 
    1200     196.9019    -5511.951    1121.4617   -2118.4942    7602.4591 
    1300    202.98293   -5433.6794    1194.3592   -1897.1579    7067.1876 
    1400    212.86876   -5411.3798    1276.3809   -1678.7668    8867.2713 
    1500    221.26247   -5359.7405    1390.3889   -1416.2668    6939.8559 
    1600     228.1783   -5288.5782    1375.3053   -1280.3883    9387.8277 
    1700    234.74001   -5255.1136    1192.2292   -1354.2862    7400.1124 
    1800     244.1285   -5282.2876    1386.5554   -1078.8029    9473.6491 
    1900    253.62148   -5158.5569    1242.3041   -989.78669    8596.2722 
    2000    260.24011   -5157.2005    1477.2039   -677.16002    9136.1769 
    2100    263.80129   -5096.4397    1403.9977   -648.51387    9640.0807 
    2200    278.10721     -5098.89    1545.7716   -344.11827    8509.7183 
    2300    278.05084    -5053.818     1495.944   -349.52438     10299.97 
    2400    287.92949   -5011.3524    1527.0261   -161.98978    8854.8877 
    2500    302.37248    -4957.687    1700.6563    231.95939    10617.134 
Loop time of 18.6761 on 1 procs for 2500 steps with 3872 atoms

Performance: 11.566 ns/day, 2.075 hours/ns, 133.861 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 17.06      | 17.06      | 17.06      |   0.0 | 91.35
Bond    | 0.73068    | 0.73068    | 0.73068    |   0.0 |  3.91
Neigh   | 0.63671    | 0.63671    | 0.63671    |   0.0 |  3.41
Comm    | 0.10272    | 0.10272    | 0.10272    |   0.0 |  0.55
Output  | 0.00064976 | 0.00064976 | 0.00064976 |   0.0 |  0.00
Modify  | 0.098028   | 0.098028   | 0.098028   |   0.0 |  0.52
Other   |            | 0.04742    |            |       |  0.25

Nlocal:        3872.00 ave        3872 max        3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        11793.0 ave       11793 max       11793 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:       770411.0 ave      770411 max      770411 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 770411
Ave neighs/atom = 198.96978
Ave special neighs/atom = 3.9669421
Neighbor list builds = 33
Dangerous builds = 0
write_data molecular-mix.data
System init for write_data ...
Total wall time: 0:00:22
